PICARA, an Analytical Pipeline Providing Probabilistic Inference about A Priori Candidates Genes Underlying Genome-Wide Association QTL in Plants
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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/545939"], "description"=>"<p>Enrichment analysis pipeline, and the data that is required in the procedure.</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology", "Computational biology"], "article_id"=>216431, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Charles Chen", "Genevieve DeClerck", "Feng Tian", "William Spooner", "Susan McCouch", "Edward Buckler"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0046596.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enrichment_analysis_pipeline_and_the_data_that_is_required_in_the_procedure_/216431", "title"=>"Enrichment analysis pipeline, and the data that is required in the procedure.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:47:11"}
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  • {"files"=>["https://ndownloader.figshare.com/files/546095"], "description"=>"<p>NAM GWAS associations identify a few cases of family specific QTL, while QTL found in previous joint-linkage analysis are mostly shared by 7 or 8 families.</p>", "links"=>[], "tags"=>["qtls", "nam"], "article_id"=>216588, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Charles Chen", "Genevieve DeClerck", "Feng Tian", "William Spooner", "Susan McCouch", "Edward Buckler"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0046596.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_distribution_of_association_QTLs_across_NAM_families_/216588", "title"=>"The distribution of association QTLs across NAM families.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:49:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/546153"], "description"=>"<p>Averaged positive and negative allelic effects and their standard deviations in tropical versus temperate NAM populations.</p>", "links"=>[], "tags"=>["allelic", "deviations", "temperate", "nam"], "article_id"=>216640, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Charles Chen", "Genevieve DeClerck", "Feng Tian", "William Spooner", "Susan McCouch", "Edward Buckler"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0046596.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Averaged_positive_and_negative_allelic_effects_and_their_standard_deviations_in_tropical_versus_temperate_NAM_populations_/216640", "title"=>"Averaged positive and negative allelic effects and their standard deviations in tropical versus temperate NAM populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:50:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/546219"], "description"=>"<p>Maize flowering time related homologs, resulted from the comparison between <i>Arabidopsis</i> and maize genes by Compara pipeline.</p>", "links"=>[], "tags"=>["flowering", "resulted", "maize", "genes", "compara"], "article_id"=>216709, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Charles Chen", "Genevieve DeClerck", "Feng Tian", "William Spooner", "Susan McCouch", "Edward Buckler"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0046596.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maize_flowering_time_related_homologs_resulted_from_the_comparison_between_Arabidopsis_and_maize_genes_by_Compara_pipeline_/216709", "title"=>"Maize flowering time related homologs, resulted from the comparison between <i>Arabidopsis</i> and maize genes by Compara pipeline.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:51:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/546271"], "description"=>"<p>The comparison of estimated linkage block sizes with perfect linkage (<i>r<sup>2</sup></i> = 1), high linkage (1><i>r<sup>2</sup></i>≥0.8), intermediate linkage (1><i>r<sup>2</sup></i>≥0.6 and 0.4) and low linkage (1><i>r<sup>2</sup></i>≥0.2).</p>", "links"=>[], "tags"=>["linkage", "sizes", "intermediate"], "article_id"=>216765, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Charles Chen", "Genevieve DeClerck", "Feng Tian", "William Spooner", "Susan McCouch", "Edward Buckler"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0046596.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_comparison_of_estimated_linkage_block_sizes_with_perfect_linkage_r_2__1_high_linkage_1_r_2_0_8_intermediate_linkage_1_r_2_0_6_and_0_4_and_low_linkage_1_r_2_0_2_/216765", "title"=>"The comparison of estimated linkage block sizes with perfect linkage (<i>r<sup>2</sup></i> = 1), high linkage (1><i>r<sup>2</sup></i>≥0.8), intermediate linkage (1><i>r<sup>2</sup></i>≥0.6 and 0.4) and low linkage (1><i>r<sup>2</sup></i>≥0.2).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:52:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/546341"], "description"=>"<p>Maize flowering time priori candidate genes are identified via enrichment of GWAS associations; and, the annotations are taken from their orthologous relationship to <i>Arabidopsis</i> genes.</p>", "links"=>[], "tags"=>["flowering", "priori"], "article_id"=>216835, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Charles Chen", "Genevieve DeClerck", "Feng Tian", "William Spooner", "Susan McCouch", "Edward Buckler"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0046596.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maize_flowering_time_priori_candidate_genes_/216835", "title"=>"Maize flowering time priori candidate genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:53:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/546446"], "description"=>"<p>In (a), the top panel shows the days-to-silk GWAS signals; blue triangles are the positive QTLs, the red are negative ones and the light blue ones at the bottom indicative of insignificant SNPs that did not pass RMIP test. SNP density along the chromosome is in grey bars in the background and significance level of RIMP scores is in the axis on the left. The gene density, calculated from the number of maize gene in every 200K bp, are in the lower panel, while the black triangles on the bottom of the density distribution mark the positions of maize flowering time homologs. Two dashed vertical lines indicate the positions of the examples in two top enriched flowering time maize homologs. (b) The enrichment of maize flowering time priori candidate: GRMZM2G115960. In this case, the co-localizing significant QTLs found in GWAS are all within the linkage block of the <i>a priori</i> candidate. (c) The enrichment of maize flowering time priori candidate: GRMZM2G365688. Three (solid red dots) of 6 significantly QTLs reside within linkage block of <i>a priori</i> candidate; the 3 unfilled red dots outside of the dashed red lines are significant, but unlinked, GWAS associations, while black dots being maize Hapmap 1 SNPs.</p>", "links"=>[], "tags"=>["GWAS", "flowering", "homologs", "maize", "chromosome"], "article_id"=>216937, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Charles Chen", "Genevieve DeClerck", "Feng Tian", "William Spooner", "Susan McCouch", "Edward Buckler"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0046596.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SNPs_GWAS_associations_flowering_time_homologs_and_gene_density_on_maize_chromosome_3_/216937", "title"=>"SNPs, GWAS associations, flowering time homologs and gene density on maize chromosome 3.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:55:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/546514"], "description"=>"<p>1: maize flowering time orthologs; 2: maize leaf genes (in Feng <i>et </i><i>al</i>. 2010); 3: maize miRNA target leaf genes; 4: biosynthetic process (GO:0009058); 5: developmental process (GO:0032502); 6: enzyme regulator activity (GO:0030234); 7: growth (GO:0040007); 8: negative regulation of response to stimulus (GO:0048585); 9: positive regulation of response to stimulus (GO:0050729) and 10: transcription regulator activity (GO:0030528). GO terms in 6 and 10 are from molecular function GO terms, while the rest of the GO terms come from biological process.</p>", "links"=>[], "tags"=>["enrichment", "lod", "scores", "curation"], "article_id"=>217003, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Charles Chen", "Genevieve DeClerck", "Feng Tian", "William Spooner", "Susan McCouch", "Edward Buckler"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0046596.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flowering_time_variation_association_enrichment_LOD_scores_comparison_in_different_curation_categories_/217003", "title"=>"Flowering time variation association enrichment LOD scores comparison in different curation categories.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 01:56:43"}

PMC Usage Stats | Further Information

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Relative Metric

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